# Fst-Heterozygosity Smoothed Quantiles

## Documentation for package ‘fsthet’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

allele.counts | This counts the number of alleles at a locus.
bins | Example heterozygosity bins from fsthet.
calc.actual.fst | This calcualtes global Fsts from a genepop dataframe.
calc.allele.freq | This calculates allele frequencies.
calc.betahat | This calculates beta-hat, the Fst value used in Lositan.
calc.exp.het | This calculates expected heterozygosities.
calc.fst | This calculates Fst.
calc.theta | This calculates theta.
ci.means | This calculates the average confidence intervals from multiple bootstrap outputs.
cis | Example dataframe of smoothed quantiles from fsthet
cis.list | Example list of CI matrices from bootstrap output from numerical simulations
fhetboot | This is a wrapper to run the bootstrapping and plot the confidence intervals and significant loci.
find.outliers | This identifies all of the SNPs outside of the smoothed quantiles in the dataset.
find.quantiles | Generates quantiles from binned Fst values
fst.boot | This is the major bootstrapping function to calculate confidence intervals.
fst.boot.means | Calculates mean values within the bins.
fst.boot.onecol | This bootstraps across all individuals to calculate a bootstrapped Fst for a randomly-sampled locus.
fst.options.print | This prints the options for choosing an Fst calculation.
fsthet | This is a wrapper to generate and plot the smoothed quantiles and identify outliers.
fsts | Example fst calculations from a genepop file.
fsts.beta | Example fst calculations from a genepop file.
fsts.betahat | Example fst calculations from a genepop file.
fsts.theta | Example fst calculations from a genepop file.
gpop | Example genepop file from numerical simulations
make.bins | This sorts Fst values into a designated number of overlapping heterozygosity bins.
my.read.genepop | This reads a genepop file into R
p.boot | Calculates mean values within the bins.
plotting.cis | This plots a dataframe of fsts with bootstrapped confidence intervals.
quant.out | Example fsthet output based on numerical simulations
remove.spaces | This removes spaces from a character vector
var.fst | This calculates Cockerham & Weir's Beta.